Genomic technologies have led to tremendous gains in understanding how pathogens
function, evolve and interact. Pathogen diversity is now measurable at high precision and …

The adaptive immune system recognizes antigens via an immense array of antigen-binding
antibodies and T-cell receptors, the immune repertoire. The interrogation of immune …

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective
vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by …

A number of approaches for studying macroevolution using phylogenetic trees have been
developed in the last few years. Here, we present RPANDA, an R package that implements …

Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses
reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of …

Background Microhabitat changes are thought to be among the main drivers of
diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we …

Despite the popularity of density-based clustering, its procedural definition makes it difficult
to analyze compared to clustering methods that minimize a loss function. In this paper, we …

Widely applicable, accurate and fast inference methods in phylodynamics are needed to
fully profit from the richness of genetic data in uncovering the dynamics of epidemics …

Genealogical tree modeling is essential for estimating evolutionary parameters in population
genetics and phylogenetics. Recent mathematical results concerning ranked genealogies …

Computational models starting from large ensembles of evolutionarily related protein
sequences capture a representation of protein families and learn constraints associated to …